First Report of Southern Tomato Virus from Tomato (Solanum lycopersicum) in Greece

HomePlant DiseaseVol. 107, No. 1First Report of Southern Tomato Virus from Tomato (Solanum lycopersicum) in Greece PreviousNext DISEASE NOTE OPENOpen Access licenseFirst Report of Southern Tomato Virus from Tomato (Solanum lycopersicum) in GreeceAnthony James, Christos Andronis, Nikoleta Kryovrysanaki, Eleni Goumenaki, Kriton Kalantidis, and Konstantina KatsarouAnthony JamesInstitute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, Heraklion 70013, GreeceSearch for more papers by this author, Christos Andronishttps://orcid.org/0000-0002-6174-579XInstitute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, Heraklion 70013, GreeceSearch for more papers by this author, Nikoleta KryovrysanakiInstitute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, Heraklion 70013, GreeceSearch for more papers by this author, Eleni Goumenakihttps://orcid.org/0000-0001-8405-912XDepartment of Agriculture, School of Agricultural Sciences, Hellenic Mediterranean University, Heraklion 71004, GreeceSearch for more papers by this author, Kriton KalantidisInstitute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, Heraklion 70013, GreeceDepartment of Biology, University of Crete, Voutes University Campus, Heraklion 70013, GreeceSearch for more papers by this author, and Konstantina Katsarou†Corresponding author: K. Katsarou; E-mail Address: [email protected]https://orcid.org/0000-0003-2728-443XInstitute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, Heraklion 70013, GreeceDepartment of Biology, University of Crete, Voutes University Campus, Heraklion 70013, GreeceSearch for more papers by this authorAffiliationsAuthors and Affiliations Anthony James1 Christos Andronis1 Nikoleta Kryovrysanaki1 Eleni Goumenaki2 Kriton Kalantidis1 3 Konstantina Katsarou1 3 † 1Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, Heraklion 70013, Greece 2Department of Agriculture, School of Agricultural Sciences, Hellenic Mediterranean University, Heraklion 71004, Greece 3Department of Biology, University of Crete, Voutes University Campus, Heraklion 70013, Greece Published Online:18 Jan 2023https://doi.org/10.1094/PDIS-02-22-0250-PDNAboutSectionsView articlePDFSupplemental ToolsAdd to favoritesDownload CitationsTrack Citations ShareShare onFacebookTwitterLinked InRedditEmailWechat View articleSouthern tomato virus is a member of the genus Amalgavirus in the family Amalgaviridae. Members of this family are characterized by double-stranded RNA genomes of about 3.4 kbp (Sabanadzovic et al. 2009). Southern tomato virus (STV) was first detected in tomato (Solanum lycopersicum L.) plants in the United States and Mexico and since has been reported from many other countries. Although STV has been reported to cause asymptomatic infection, in some cultivars symptoms include interveinal necrosis, stunting, fruit discoloration, and reduced fruit size (Harju et al. 2021; Sabanadzovic et al. 2009). Transmission of STV occurs vertically through infected seeds (Sabanadzovic et al. 2009), and to date no virions have been identified in infected plants. In 2019, tomato seedlings from a breeding collection in Crete (Greece) were assessed for the presence of viruses using high-throughput sequencing (HTS). A total of 40 plant lines were grown, with plants pooled into two groups for HTS (pool 1 with 22 samples and pool 2 with 18 samples). RNA was extracted from leaf tissue using TRIzol (Katsarou et al. 2022), and 2 μg of RNA from each sample was pooled for HTS (Macrogen, the Netherlands). Assembly of raw reads was carried out using metaSPAdes (Nurk et al. 2017). BLASTn analysis against RVDBv20.0 (Goodacre et al. 2018) of the contigs from pool 1 did not result in any sequences matching plant viruses. In contrast, BLASTn of the assembled contigs from pool 2 (NCBI SRA: BioProject PRJNA818693) identified three small contigs of 336, 307, and 230 nt, respectively, with 98 to 100% nucleotide sequence identity to STV. Mapping to the STV reference genome sequence (GenBank accession no. NC_011591) using Geneious R7 confirmed 54 reads that mapped to the STV genome. To confirm the presence of STV in the tomato plants from pool 2, reverse transcription PCR was carried out using the RNA extracts previously prepared for HTS. Two sets of PCR primers were designed, STV_F (5′-TATATTGGAGGAGGAGGCGGT-3′) and STV_R (5′-ATATTCCTTCACCCTGCGCC-3′), which were predicted to amplify a 658-nt region of the RdRP gene, and a second set of nested primers, STVnF (5′-TGGAGATGAGGTGCTCGAAGA-3′) and STVnR (5′-TGGCTATGATGTATCTGTGCTTGA-3′), which amplify 458 nt within the first-round target region. Complementary DNA was synthesized using M-MuLV reverse transcriptase (Minotech, Greece), and two rounds of PCR were subsequently carried out using Taq DNA polymerase (EnzyQuest, Greece) as per the manufacturer’s recommendations. Analysis of the PCR products confirmed the presence of amplicons in three samples. The second-round PCR amplicons from the three samples were excised, gel-purified, and Sanger-sequenced (Genewiz, Germany). The trimmed reads (351 nt) were identical to each other, and BLASTn analysis confirmed their identity as STV, with the Crete sequences identical to three isolates from Germany (MK948545) and Switzerland (MF422617 and MF422618). This is the first report of STV in Greece. STV is seed transmitted but often causes no apparent symptoms in infected plants. This is the likely explanation for infected plants to be present in the breeding collection assessed in this study. Knowledge that these plants are not coinfected with other viruses may assist further work to identify symptoms associated with STV infection, as mixed infections are common in previous reports, as well as further investigate plant-host interactions between STV and tomato. Further work is now required to assess the field occurrence, yield effects, or other impacts of STV infections in tomato crops in Crete.The author(s) declare no conflict of interest.References:Goodacre, N., et al. 2018. mSphere 3:e00069-18. https://doi.org/10.1128/mSphereDirect.00069-18 Crossref, Google ScholarHarju, V., et al. 2021. New Dis. Rep. 43:e12014. https://doi.org/10.1002/ndr2.12014 Crossref, Google ScholarKatsarou, K., et al. 2022. Page 287 in: Viroids. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-1464-8_24 Google ScholarNurk, S., et al. 2017. Genome Res. 27:824. https://doi.org/10.1101/gr.213959.116 Crossref, ISI, Google ScholarSabanadzovic, S. I., et al. 2009. Virus Res. 140:130. https://doi.org/10.1016/j.virusres.2008.11.018 Crossref, ISI, Google ScholarFunding: The authors would like to thank the operation “Development of an Integrated System for Detection of Plant Pathogens in the Field” with code OPS MIS5022230 and the Operational Program “Crete 2014-20” under the context of NSRF 2014-2020, co-financed by Greece and the European Union (European Structural and Investment Funds). General Secretariat of Research and Technology, project “Emblematic Action for Research in the Cretan Agrofood Sector: Four Institutions, Four References” (AGRO4CRETE—2018SE01300000) is also gratefully acknowledged. Funding of this project came from a category C grant entitled ‘The Effect of Changes in Rural Communities May Affect the Plant-Pathogen Interactions’ KA10894-Special Account for Research Funds of University of Crete.The author(s) declare no conflict of interest.DetailsFiguresLiterature CitedRelated Vol. 107, No. 1 January 2023SubscribeISSN:0191-2917e-ISSN:1943-7692 Download Metrics Article History Issue Date: 1 Feb 2023Published: 18 Jan 2023Accepted: 17 May 2022 Page: 237 Information© 2023 The American Phytopathological SocietyFundingNSRF 2014-2020Grant/Award Number: 2014-20Greece and the European Union (European Structural and Investment Funds)General Secretariat of Research and TechnologyAGRO4CRETEGrant/Award Number: 2018SE01300000University of CreteGrant/Award Number: KA10894KeywordsAmalgaviridaehigh-throughput sequencingvegetablesvirusThe author(s) declare no conflict of interest.PDF download